Data and code from Rodkey et al. (2024): "Sod farms drive habitat selection of a migratory grassland shorebird during a critical stopover period"

The data and code in this repository was used to fit the final models for the submitted manuscript "Sod farms drive habitat selection of a migratory grassland shorebird" by Rodkey and coauthors.

Abstract:

Migratory shorebirds are one of the fastest declining groups of North American avifauna. Yet, relatively little is known about how these species select habitat during migration. We explored the habitat selection of Buff-breasted Sandpipers (Calidris subruficollis) during spring and fall migration through the Texas Coastal Plain, a major stopover region for this species. Using tracking data from 118 birds compiled over 4 years, we found Buff-breasted Sandpipers selected intensively managed crops such as sod and short-stature crop fields, but generally avoided rangeland and areas near trees and shrubs. This work supports prior studies that also indicate the importance of short-stature vegetation for this species. Use of sod and corn varied by season, with birds preferring sod in spring, and avoiding corn when it is tall, but selecting for corn in fall after harvest. This dependence on cropland in the Texas Coastal Plain is contrary to habitat use observed in other parts of their non-breeding range, where rangelands are used extensively. The species' almost complete reliance on a highly specialized crop, sod, at this critical stopover site raises concerns about potential exposure to contaminants as well as questions about whether current management practices are providing suitable conditions for migratory grassland birds.

Data and code for model fitting     bbsa_sodfarm_selection.zipFollowing files are used to fit final models for the Texas study and the range-wide study.

script_tx is the script used to fit models on Texas dataset.   script_tx.R

script_rw  is the script used to fit models on range-wide dataset.  script_rw.R

data_tx is the datafile for containing model input data for the Texas models.  data_tx.csv

data_rw is the datafile containing model input data for the rangewide models.  data_rw.csv

Columns in the datafiles for both Texas and rangewide models (data_tx and data_rw) are organized as follows:

ID - unique identifier for tracked birds

year - year in which bird was tracked

season - season in which bird was tracked (spring or fall)

fromTexas - (rangewide dataset only) whether or not the tracked bird was captured in the study region, the Texas Coastal Plain (T = bird was caught within study region; F = bird was caught outside of study region)

night- (Texas dataset only) whether or not the location fell within daytime or nightime hours (y = nightime, n = daytime)

droad - distance of location in meters from nearest road

dwoody - distance of location in meters from nearest woody cover

corn_prop250 - proportion of corn/sorghum landcover type within a 250m buffer around location

cotton_prop500 - proportion of cotton/soybean landcover type within a 500m buffer around location

herb_prop250 - proportion of herbaceous (i.e., grassy) landcover type within a 250m buffer around location

rice_prop1000 - proportion of rice landcover type within a 1000m buffer around location

sod_prop250 - proportion of sod landcover type within a 250m buffer around location

presence - identifying used versus available locations (1 = used, as in, an actual GPS location of tracked bird; 0 = available, as in, a randomly generated location within the bird's area of use)

Tracking data     bbsa_txStudy_movebank_20240731.csv

Tracking data used for Texas study. Lotek PinPoint GPS data were imported and decoded via Movebank and relevant columns were selected. Columns are organized as follows:

timestamp - time of GPS location in UTC (format = YYYY-MM-DD HH:MM:SS.SSS)

location.long - longitude of GPS location in decimal degrees, projected in the WGS 84 datum

location.lat - latitude of GPS location in decimal degrees, projected in the WGS 84 datum

lotek.crc.status.text - value of Lotek's cyclical redundancy check (OK = good data, OK(corrected) = message was corrected with Lotek's error correction algorithm, Fail = data has been corrupted on transmission, and therefore cannot be trusted)

sensor.type - type of sensor, all rows are "gps"

tag.local.identifier - Argos ID of the attached Lotek PinPoint GPS transmitter

individual.local.identifier - unique individual identifier, in this case the USGS-issued band number attached to each tracked bird

individual.taxon.canonical.name - species  taxonomical name, all rows are "Calidris subruficollis"

sex - sex of tracked bird (M = male, F = female)

age - age of tracke bird (AHY = after-hatch-year, HY = hatch-year)

Sod farm layer      sodLayer_tgcp.tifRaster layer representing sod farms in the Western Gulf Coastal Plain ecoregion of Texas. Resolution of 30m with values from 0 - 1, with 1 representing sod farms. Sod farms were identified via visual inspection, cross-referencing the U.S. Department of Agriculture's Cropland Data Layer with Google Earth high resolution imagery from 2022. This was a modification of preliminary data on sod farm distribution in the region compiled by B. Ortego, S. Gifford and J. Lyons.